And the problem WAS in large part the methods because if their methods had been good, they would not have found NOTHING.

I invite you to carefully read Gerwyn and company's rebuttal in Retrovirology, to understand, once and for all, why NONE of the negative studies are worth the paper they are written on, because their methods were bad.

Although three MLVs were found one MLV dominated the rest, infecting 86% of the CFS patients. One of the MLVs was found also in one healthy control. They are talking about gag gene sequences.

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Your point being?

What is going with XMRV itself is not as important as it was before the Alter paper

Are you kidding?

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No, not at all. Since they have now found 4 MLV's one of which is XMRV - then the singular fact that XMRV is present is not as important as it was before the paper. The most salient fact is that there are a swarm of MLV's present in CFS. Which part of that don't you get?

While the WPIs overall thesis was confirmed we still have two disparate findings; the WPI found XMRV and no other MLVs while the Lo/Alter group found no XMRV and several other MLVs. Researchers abhor impasses like this and they must eventually be cleared up. That the virus is exceedingly tricky is clear.

you just don't get it, do you

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I don't V99 - those are the facts. Did Alter find XMRV? No.......Does that mean that at some point the two findings have to be reconciled? Yes, do you disagree with that? (How can you disagree with that??)

Its possible but hardly likely that both findings are correct. Its more likely, I would guess, based on the swarm thesis, that the problem lies with the WPI findings rather than Dr. Alters.

Wow!!!! Both findings are likely correct. Alter has completely vindicated the WPI, what are you trying to do Cort? This is way out of order.

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I almost feel like we are different planets reading different papers. Are you saying that the WPI group does not have other MLV's in it? And that the ALter group does not have XMRV? Actually I will change that sentence to the problem probably lies in both groups. XMrV and MLV's are probably present in both groups. A complete vindication would be Alter findings XMRV in his samples. That would have set the research world afire. We'll know when that happens.

I don't know if I can bear to read the rest of it. I wouldn suggest you don't bother ever again. You are doing a disservice to every patient with the disease by posting nonsense like this.

The FDA response did not, interestingly, suggest that they believed other problems with methodology played a role.

Yes they did, here:

"Indeed, it is possible that the PCR primers used in various studies may have different sensitivity in detecting the diverse group of MLV-related virus gag gene sequences that we found in the clinical samples. The 5′ gag leader sequence of previously described XMRVs represents the most divergent segment of the XMRV genome in comparison with the genomes of the other MLVs (4). In particular, there is evidently a unique 15-nt deletion in the 5′ gag leader region in all of the XMRVs previously identified in patients with prostate cancer and CFS (3, 4). To detect XMRVs in human samples with better sensitivity and specificity, some studies used a PCR primer spanning this unique deletion as the XMRV-specific primer (6). However, none of the viral gag gene sequences amplified from the blood samples of CFS patients and blood donors in our study has this particular deletion (Fig. S1). As a consequence, such primers might have been insensitive in detecting the MLV-related gag gene sequences that we have identified." Lo et al.

"Indeed, it is possible that the PCR primers used in various studies may have different sensitivity in detecting the diverse group of MLV-related virus gag gene sequences that we found in the clinical samples. The 5′ gag leader sequence of previously described XMRVs represents the most divergent segment of the XMRV genome in comparison with the genomes of the other MLVs (4). In particular, there is evidently a unique 15-nt deletion in the 5′ gag leader region in all of the XMRVs previously identified in patients with prostate cancer and CFS (3, 4). To detect XMRVs in human samples with better sensitivity and specificity, some studies used a PCR primer spanning this unique deletion as the “XMRV-specific” primer (6). However, none of the viral gag gene sequences amplified from the blood samples of CFS patients and blood donors in our study has this particular deletion (Fig. S1). As a consequence, such primers might have been insensitive in detecting the MLV-related gag gene sequences that we have identified." Lo et al.

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Dr. Lo in the Press Conference did not say anything about this - and neither did the FDA response which I noted was what I was referring to. Dr. Alter repeatedly referred to the fact that CFS is a spectrum disorder.

10. How are the differences between the CDC and FDA study results being evaluated?
Differences in the results could reflect differences in the patient populations that provided the samples. Alternatively, undefined differences in the method of sample preparation could be contributing to the discordant test results. All of the scientists involved are working collaboratively to design experiments to quickly answer this scientifically puzzling question. An independent investigator at the National Heart, Lung, and Blood Institute (NHLBI) set up a test set of 36 samples, including known positives and presumed negatives. Both the FDA/NIH and CDC labs participated in this test, and the results showed that both labs were able to detect XMRV present at low levels in blinded samples. Additionally, the CDC laboratory provided 82 samples from their published negative study to FDA, who tested the samples blindly. Initial analysis shows that the FDA test results are generally consistent with CDC, with no XMRV-positive results in the CFS samples CDC provided (34 samples were tested, 31 were negative, 3 were indeterminate).

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However you have a good point. My thought was that sample preparation was a simple factor but it turns out that its not. In any case I am committed to getting to the bottom of this.

The Alter/Lo group did not do that, citing the difficulty of having to wade through from hundreds to 1,000’s of cells in order to find the one infected with MLV’s. (Yes, it is very rare in the blood!).

That's is not accurate. I cannot find the source right now, but that makes them sound lazy. They only believed that there was no reason to delay the paper.

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You're the one that's interpreting that as "lazy'. I interpret that as having not enough time - and it is accurate.

This study was a big breakthrough. It demonstrates that there are most likely problems with the other studies

Basically it comes down to this:all the CDC patients in the Switzer et al study are empiric criteria patients. Within any study that uses the empiric criteria, there may well be patients who satisfy the Fukuda criteria. But patients were chosen using the empiric criteria.

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My question is how much does it matter?They picked patients then that met both the empiric and the Fukuda criteria. Everyone on this board probably meets the Empirical criteria and the Fukuda criteria and the Canadian criteria. So long as they had Fukuda patients in that subset (which, as I pointed out is not necessarily true) then the fact that they almost met a weaker criteria is not that relevant to me.

10. How are the differences between the CDC and FDA study results being evaluated?

Differences in the results could reflect differences in the patient populations that provided the samples. Alternatively, undefined differences in the method of sample preparation could be contributing to the discordant test results. All of the scientists involved are working collaboratively to design experiments to quickly answer this scientifically puzzling question. An independent investigator at the National Heart, Lung, and Blood Institute (NHLBI) set up a test set of 36 samples, including known positives and presumed negatives. Both the FDA/NIH and CDC labs participated in this test, and the results showed that both labs were able to detect XMRV present at low levels in blinded samples. Additionally, the CDC laboratory provided 82 samples from their published negative study to FDA, who tested the samples blindly. Initial analysis shows that the FDA test results are generally consistent with CDC, with no XMRV-positive results in the CFS samples CDC provided (34 samples were tested, 31 were negative, 3 were indeterminate).

Disagree. I would like to point out that Cort has made some objective observations that make sense. Maybe you don't agree with all of them, or they are not what you want them to be, but his analysis makes sense based on the limited knowledge we actually have.

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That's a good point. I did the best with my ability with what I had, It turns out that Andrea was right, though; I did miss a very important piece of the puzzle and I am rectifying that now - it should be up soon.

I agree that cohort was a big part of the problem, but the methods were also bad. Cohort definition had nothing to do wih finding ZERO in their controls, when we now have peer reviewed papers showing a possible prevalence of 1.7% in Japan, almost 3% in Northern Germany, the WPI's 4% and Alter's 6.8%. If their methods had been good, they would have found something.

My question is how much does it matter?They picked patients then that met both the empiric and the Fukuda criteria. Everyone on this board probably meets the Empirical criteria and the Fukuda criteria and the Canadian criteria. So long as they had Fukuda patients in that subset (which, as I pointed out is not necessarily true) then the fact that they almost met a weaker criteria is not that relevant to me.

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I'm exactly sure what you are saying.
I initially picked up on your statement:

Some of the CDC samples also came from people meeting the Empirical definition which increased prevalence rates dramatically and ushered in a new breed of ‘CFS’ patient.

We don't know anything about what criteria they satisfy except that they all satisfied the empiric criteria.
And not just the CDC but also Lo couldn't find any XMRV/MLVs in them.

This is a great way to bash the empiric criteria. So I just pointed out that it is more accurate to say that they all satisfy the empiric criteria.
The empiric criteria have turned up in all sorts of psychobabble e.g. personality disorders, childhood abuse studies, rate of current and lifetime psychiatric disorders (89% were found to have lifetime psychiatric disorders and the CDC recommended more CFS patients need to see psychiatrists based on this study).
I think it is an important issue.
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ETA: It is relevant because it shows the difference between the patients Komaroff, Cheney & Bell see and the empiric criteria that make up CDC studies. It shows that the CDC are not using patients that are representative of the CFS patients specialists are seeing. You did sort of make the point and I am pleased you did. But you asked above so I'm explaining it.

I perfectly understand how you made the mistake as the Switzer article isn't clear.
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ETA: the CDC say that the empiric criteria are the Fukuda criteria. But nobody else says that. People can get tricked when they say patients satisfied the Fukuda criteria.
If one says these patients satsify the Fukuda criteria patients, one should also says that applies to the two childhood abuse studies, the prevalence study that found 2.54%, the study that found a higher rate of personality disorders, the study that found 57% current psychiatric disorders and 89% lifetime psychiatric disorders, etc. The CDC says they used the Fukuda criteria for them as they say the empiric criteria are just a version of them. I think we need to emphasise to people over and over that empiric criteric are a very specialised set of criteria and we shouldn't call them Fukuda criteria.

Although three MLVs were found one MLV dominated the rest, infecting 86% of the CFS patients. One of the MLVs was found also in one healthy control.

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They found gag gene sequences, not more than that as you imply.

What is going with XMRV itself is not as important as it was before the Alter paper

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No, not at all. Since they have now found 4 MLV's one of which is XMRV - then the singular fact that XMRV is present is not as important as it was before the paper. The most salient fact is that there are a swarm of MLV's present in CFS. Which part of that don't you get?

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They found sequences, they would not have been looking if it were not for the 'Science' paper. You are jumping to conclusions about XMRV. It will most likely be found to also be mutating. You haven't thought this through. They also found three different types of MLV-related virus gag gene sequences in patients, and one in a control. XMRV is then another relative. That makes 5

While the WPIs overall thesis was confirmed we still have two disparate findings; the WPI found XMRV and no other MLVs while the Lo/Alter group found no XMRV and several other MLVs. Researchers abhor impasses like this and they must eventually be cleared up. That the virus is exceedingly tricky is clear.

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I don't V99 - those are the facts. Did Alter find XMRV? No.......Does that mean that at some point the two findings have to be reconciled? Yes, do you disagree with that? (How can you disagree with that??)

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Well firstly Harvey Alter disagrees with that. He says they are not 'disparate findings'. The finding of other MLV sequences supports the finding of XMRV. It's that simple. It all fits, if they are mutating.

Its possible but hardly likely that both findings are correct. Its more likely, I would guess, based on the swarm thesis, that the problem lies with the WPI findings rather than Dr. Alters.

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I almost feel like we are different planets reading different papers. Are you saying that the WPI group does not have other MLV's in it? And that the ALter group does not have XMRV? Actually I will change that sentence to the problem probably lies in both groups. XMrV and MLV's are probably present in both groups. A complete vindication would be Alter findings XMRV in his samples. That would have set the research world afire. We'll know when that happens.

I don't know if I can bear to read the rest of it. I wouldn suggest you don't bother ever again. You are doing a disservice to every patient with the disease by posting nonsense like this.

The FDA response did not, interestingly, suggest that they believed other problems with methodology played a role.

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Again I will direct you to Alter & Lo's comments. How on earth would finding similar MLV sequences rub out the existence of XMRV? because that is what you are saying. I'm saying what they have been saying, that they are finding them also. Cort, what problem are you talking about? There is no problem. Both studies back each other up. You have no idea what you are talking about. Your making it up.

The genetic sequences Lo and Alter looked for were the same as the genetic sequences that all the other studies looked for. The Lombardi (WPI), Groom, McClure and Switzer (CDC) papers all looked for gag sequences identified by primer #s 419F/1154R. (Dr. Racaniello noted that everyone had tried to duplicate the WPIs results by looking for the same sequence and they did.)

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I didn't make the statement that they are looking at the same genetic sequence

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No, if you read the sentence I am clearly saying that you are misleading people into thinking that these were replication studies, and you should have expanded on this to explain why the method employed can still be wrong.

Yes they did, here:
"Indeed, it is possible that the PCR primers used in various studies may have different sensitivity in detecting the diverse group of MLV-related virus gag gene sequences that we found in the clinical samples. The 5′ gag leader sequence of previously described XMRVs represents the most divergent segment of the XMRV genome in comparison with the genomes of the other MLVs (4). In particular, there is evidently a unique 15-nt deletion in the 5′ gag leader region in all of the XMRVs previously identified in patients with prostate cancer and CFS (3, 4). To detect XMRVs in human samples with better sensitivity and specificity, some studies used a PCR primer spanning this unique deletion as the “XMRV-specific” primer (6). However, none of the viral gag gene sequences amplified from the blood samples of CFS patients and blood donors in our study has this particular deletion (Fig. S1). As a consequence, such primers might have been insensitive in detecting the MLV-related gag gene sequences that we have identified." Lo et al.

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You replied

Dr. Lo in the Press Conference did not say anything about this - and neither did the FDA response which I noted was what I was referring to. Dr. Alter repeatedly referred to the fact that CFS is a spectrum disorder.

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That's because it is from the PNAS paper, Lo et al. The one you should have read.

I agree that cohort was a big part of the problem, but the methods were also bad. Cohort definition had nothing to do wih finding ZERO in their controls, when we now have peer reviewed papers showing a possible prevalence of 1.7% in Japan, almost 3% in Northern Germany, the WPI's 4% and Alter's 6.8%. If their methods had been good, they would have found something.

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If something has a 1% chance of happening, the chances of it not happening in 104 goes is (.99)^104=0.3516.

If something has a 2% chance of happening, the chances of it not happening in 104 goes is (.98)^104=0.1223.

You're the one that's interpreting that as "lazy'. I interpret that as having not enough time - and it is accurate.

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No, that is what you are implying. They could have created enough time, they didn't give that as an explanation for not doing the additional experiments. As you say you are interpreting, I will find that quote and show you.

You have now put a comment I made in a quote box, this one:

This study was a big breakthrough. It demonstrates that there are most likely problems with the other studies

They found sequences, they would not have been looking if it were not for the 'Science' paper. You are jumping to conclusions about XMRV. It will most likely be found to also be mutating. You haven't thought this through. They also found three different types of MLV-related virus gag gene sequences in patients, and one in a control. XMRV is then another relative. That makes 5

Well firstly Harvey Alter disagrees with that. He says they are not 'disparate findings'. The finding of other MLV sequences supports the finding of XMRV. It's that simple. It all fits, if they are mutating.

Again I will direct you to Alter & Lo's comments. How on earth would finding similar MLV sequences rub out the existence of XMRV? because that is what you are saying. I'm saying what they have been saying, that they are finding them also. Cort, what problem are you talking about? There is no problem. Both studies back each other up. You have no idea what you are talking about. Your making it up

No, if you read the sentence I am clearly saying that you are misleading people into thinking that these were replication studies, and you should have expanded on this to explain why the method employed can still be wrong.

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I think you are (intentionally) misunderstanding what I'm saying. Who said XMRV was rubbed out? My intent was that the WPI missed part of the swarm....not that XMRV does not exist - You are, once again, for the umpteenth time, putting words into my mouth. With regard to the replication problem I agree you have a point. One part of the study did replicate an important element of the study - they were all looking for the same genetic sequence. My problem is that I misunderstood the complexities of PCR. Like I said I am clearing that up.

They found sequences, they would not have been looking if it were not for the 'Science' paper.

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So????

I think you're uncomfortable with subtleties. I noted very clearly that the Alter paper and Harvey Alter himself stated that his findings validated the general findings of the Science paper. Did you miss this?

They did in the most important sense; the Alter/Lo study (Lo was the principal investigator) confirmed the major finding of the original Science paper- that retroviruses are highly prevalent in people with CFS and are found in much lower levels of the general population. After all the zeros and null findings of the previous studies, the Alter findings were remarkably consistent with the WPI's original findings (86% of CFS patients vs 68% and 7% of controls vs 4%). The fact that two accomplished researchers using their own samples and their own techniques duplicated the finding of mouse retroviruses in chronic fatigue syndrome was enormously beneficial.

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They obviously did not confirm the presence of XMRV....If they didn't do that do you suggest that I act as if they did?

No, if you read the sentence I am clearly saying that you are misleading people into thinking that these were replication studies, and you should have expanded on this to explain why the method employed can still be wrong.

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This is what I wrote:

The genetic sequences Lo and Alter looked for were the same as the genetic sequences that all the other studies looked for. The Lombardi (WPI), Groom, McClure and Switzer (CDC) papers all looked for ‘gag’ sequences identified by primer #’s 419F/1154R. (Dr. Racaniello noted that everyone had tried to duplicate the WPI’s results by looking for the same sequence and they did.)

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That is not untrue - they all did look for that sequence. In fact I did miss something - as I noted earlier - about that - and I am clearing it up. The second sequence, as it turns out, is the determinative one.